BUD13 RNA-Seq in HepG2

General Information


RBP	BUD13
Cell_Line	HepG2
Method	shRNA
Exp_Name	BUD13-BGHLV30-HepG2
ENCODE_series_ID	ENCSR662ZKE
Batch_ID	BGHLV30
Pool ID	Pool-151215B
Local_Set_Name	set30
ENCODE_KD_Exp_ID	ENCSR382QKD
ENCODE_CN_Exp_ID	ENCSR067GHD
Rep1	BUD13_BGHLV30-17
Rep2	BUD13_BGHLV30-18
CN1	NT_BGHLV30-1
CN2	NT_BGHLV30-2
Rep1_qPCR	81.4
Rep2_qPCR	68.4
Rep1_WB	88.6
Rep2_WB	72.4
Antibody Cat#	A303-320A
Antibody Lot#	A303-320A
Antibody DCC ID	ENCAB673IND
Status	Released
Project	ENCODE3
ID	682

Experiment Information (Status: Released)

	BGHLV30-17	BGHLV30-18
idx	701	702
TRCN#_or_BGC#	TRCN0000074896	TRCN0000074896
shRNA_or_gRNA_sequence	CGAGTATCTGAAGCGTTACTT	CGAGTATCTGAAGCGTTACTT
PAM
Name	BUD13	BUD13
Sample_ID	BGHLV30-17	BGHLV30-18
transduction_Date	8/25/2015	8/25/2015
days
RBP_name	BUD13	BUD13
qPCR_result	81.4	68.4
Ave_qPCR	74.9
RT-qPCR_primer-F	ctttcgttccagtgccaaat
RT-qPCR_primer-R	aggagatgaatccggggtat
protein_conc	4249	4348
WB_result	88.6	72.4
Ave_WB	80.5
WB_DONE_date	9/4/2015
MW	71kd
IP	1	1
antibody_Cat#	A303-320A	A303-320A
Antibody DCC ID	ENCAB673IND	ENCAB673IND
submitted_to_DCC_date	12/7/2015
Rep1_TPM	13	0
Rep2_TPM	9.8	0
Action
Library_start_date	11/5/2015	11/5/2015
repeat_library
Note	x	x
ID	2788	2789

Western Blot

RBP	Antibody Info	Primary-HepG2	Secondary-HepG2	Primary-K562	Secondary-K562	Primary-UBERON	Primary-Hela
BUD13	Product_ID: A303-320A Lot_ID: 1 Source: Bethyl Labs Target Name: BUD13-human

Experiment Status

	BGHLV30-17	BGHLV30-18
Sample_ID	BGHLV30-17	BGHLV30-18
Sample Name	BUD13_BGHLV30-17	BUD13_BGHLV30-18
Sample Name	BUD13_BGHLV30-17	BUD13_BGHLV30-18
RBP	BUD13	BUD13
Cell_Line	HepG2	HepG2
Exp UID
Status	Released	Released
Status_date	2016-03-04	2016-03-04
Project	ENCODE3	ENCODE3
Note
ID	1046	1047

Library-Prep
Sequencing

Library-Prep Information

	BGHLV30-17	BGHLV30-18
Sample #
Sample Name	BUD13-BGHLV30-17	BUD13-BGHLV30-18
Sample_Name_Alias	BUD13_BGHLV30-17	BUD13_BGHLV30-18
Index Well Position	S25	S27
Index_table	IDT_TruSeqSingleIndex_24	IDT_TruSeqSingleIndex_24
LibPrep_date	2015-11-05	2015-11-05
Lib_ID	Lib-151105	Lib-151105
Tecan_Location
Tecan
Tecan_date
Size_bp
Peak_Molarity
libSampleQC_DNA_Well	DNA_Library_LV28-29-30/set1/G9.png	DNA_Library_LV28-29-30/set1/H9.png
RIN	9.9	9.8
libSample_RNA_Well	RNA_Library_LV29-30-31-32/set1/G4.png	RNA_Library_LV29-30-31-32/set1/H4.png
SampleQC_method
SampleQC_date
Sample_ID	BGHLV30-17	BGHLV30-18
RBP	BUD13	BUD13
Batch_ID	BGHLV30	BGHLV30
WB_result	88.600	72.400
Library Description	TruSeq mRNA	TruSeq mRNA
Repeat_Library_Suffix
Lib_Status	SendToSequence	SendToSequence
Project	ENCODE3	ENCODE3
ID	2738	2739

Sequencing Information

	BGHLV30-17	BGHLV30-18
Sample_ID	BGHLV30-17	BGHLV30-18
Sample Name	BUD13_BGHLV30-17	BUD13_BGHLV30-18
Pool ID	Pool-151215B	Pool-151215B
LocalServer_folder	set30	set30
total_reads	59,551,494	79,218,606
total_aligned_reads	52,614,814	68,965,504
unique_aligned_reads	49,752,012	65,049,402
percent_uniqueAligned	0.83545	0.82114
correlation_replicates	0.997626	0.997626
spikein_reads	149,306	183,600
percent_spikeins	0.00251	0.00232
original_ReadLength	100	100
QC_Status	Submitted	Submitted
ID	1397	1398

Data Submission Information

	BGHLV30-17	BGHLV30-17
ENCODE_alias	brenton-graveley:BUD13_BGHLV30	brenton-graveley:BUD13-BGHLV30-HepG2
ENCODE_accession	ENCSR382QKD	ENCSR662ZKE
object_type	experiment	gene_silencing_series
assay_type	knockdown followed by RNA-seq	knockdown followed by RNA-seq
Sample_ID	BGHLV30-17	BGHLV30-17
Sample Name	BUD13_BGHLV30-17	BUD13_BGHLV30-17
Selected	Yes	Yes
Status	Released	Released
Status_Date	2016-03-03	2022-03-01
Project	ENCODE3	ENCODE3

protocol_URL
ID	3072	6606

File Information

file_name	file_path	file_format	output_type	assay_type	lab	Sample ID	platform	read_length	run_type	paired_end	assembly	genome_annotation	derived_from	controlled_by	Project	FILE_ID
BUD13_BGHLV30-17_ACTGAT_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1397	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20702
BUD13_BGHLV30-17_ACTGAT_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1397	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20736
BUD13_BGHLV30-17_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17_ACTGAT_L003_001.R1.fastq.gz,BUD13_BGHLV30-17_ACTGAT_L003_001.R2.fastq.gz		ENCORE2	20770
BUD13_BGHLV30-17_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	20804
BUD13_BGHLV30-17_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	20838
BUD13_BGHLV30-17_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	20872
BUD13_BGHLV30-17_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17/Aligned.sortedByCoord.out.bam		ENCORE2	20906
BUD13_BGHLV30-17_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1397					GRCh38	V40	BUD13_BGHLV30-17_ACTGAT_L003_001.R1.fastq.gz,BUD13_BGHLV30-17_ACTGAT_L003_001.R2.fastq.gz		ENCORE2	20940
BUD13_BGHLV30-18_ATTCCT_L003_001.R1.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1398	HiSeq2500	100	paired-ended	1				NT_BGHLV30-1_GTCCGC_L008_001.R1.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R1.fastq.gz	ENCODE3	20703
BUD13_BGHLV30-18_ATTCCT_L003_001.R2.fastq.gz	ENCODE_DATA/set30/fastq	fastq	reads	knockdown followed by RNA-seq	Graveley Lab	1398	HiSeq2500	100	paired-ended	2				NT_BGHLV30-1_GTCCGC_L008_001.R2.fastq.gz,NT_BGHLV30-2_GTGAAA_L008_001.R2.fastq.gz	ENCODE3	20737
BUD13_BGHLV30-18_Aligned.sortedByCoord.out.bam	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bam	alignments	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18_ATTCCT_L003_001.R1.fastq.gz,BUD13_BGHLV30-18_ATTCCT_L003_001.R2.fastq.gz		ENCORE2	20771
BUD13_BGHLV30-18_Signal.Unique.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+unique	plus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	20805
BUD13_BGHLV30-18_Signal.Unique.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-unique	minus strand signal of unique reads	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	20839
BUD13_BGHLV30-18_Signal.UniqueMultiple.strand+.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig+all	plus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	20873
BUD13_BGHLV30-18_Signal.UniqueMultiple.strand-.bw	ENCODE_DATA/set30/STAR_ENCORE2_file_links	bigWig-all	minus strand signal of all reads	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18/Aligned.sortedByCoord.out.bam		ENCORE2	20907
BUD13_BGHLV30-18_quant.sf	ENCODE_DATA/set30/salmon_ENCORE2	transcript_quantification	transcript quantifications	knockdown followed by RNA-seq	Graveley Lab	1398					GRCh38	V40	BUD13_BGHLV30-18_ATTCCT_L003_001.R1.fastq.gz,BUD13_BGHLV30-18_ATTCCT_L003_001.R2.fastq.gz		ENCORE2	20941